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- PDB-2d4d: The Crystal Structure of human beta2-microglobulin, L39W W60F W95... -

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Basic information

Entry
Database: PDB / ID: 2d4d
TitleThe Crystal Structure of human beta2-microglobulin, L39W W60F W95F Mutant
ComponentsBeta-2-microglobulinBeta-2 microglobulin
KeywordsIMMUNE SYSTEM / Immunoglobulin constant domain
Function / homology
Function and homology information


positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Beta-2-Microglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins ...Beta-2-Microglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsIwata, K. / Matsuura, T. / Nakagawa, A. / Goto, Y.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Conformation of Amyloid Fibrils of beta2-Microglobulin Probed by Tryptophan Mutagenesis
Authors: Kihara, M. / Chatani, E. / Iwata, K. / Yamamoto, K. / Matsuura, T. / Nakagawa, A. / Naiki, H. / Goto, Y.
History
DepositionOct 17, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8972
Polymers11,8741
Non-polymers231
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.423, 28.776, 57.241
Angle α, β, γ (deg.)90.00, 123.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11874.338 Da / Num. of mol.: 1 / Mutation: L39W, W60F, W95F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHIKARU1a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: P61769
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG4000, 25% glycerol, 0.2M ammonium acetate, 0.1M sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jun 24, 2005
RadiationMonochromator: conforcal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→47.673 Å / Num. all: 6345 / Num. obs: 6343 / % possible obs: 100 % / Observed criterion σ(F): 3 / Redundancy: 3.5 % / Biso Wilson estimate: 26.44 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 927 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.315 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LDS

1lds


Resolution: 2.1→47.67 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.948 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26543 294 4.6 %RANDOM
Rwork0.21571 ---
all0.21802 ---
obs0.21802 6047 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.258 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å20.59 Å2
2--0.03 Å20 Å2
3---1.91 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms804 0 1 48 853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022828
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.9381121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.741595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89523.95343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.93515143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.189154
X-RAY DIFFRACTIONr_chiral_restr0.0980.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02635
X-RAY DIFFRACTIONr_nbd_refined0.1980.2302
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2542
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.245
X-RAY DIFFRACTIONr_metal_ion_refined0.1150.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.29
X-RAY DIFFRACTIONr_mcbond_it0.8131.5482
X-RAY DIFFRACTIONr_mcangle_it1.5182790
X-RAY DIFFRACTIONr_scbond_it1.8483357
X-RAY DIFFRACTIONr_scangle_it2.9964.5331
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 31 -
Rwork0.245 444 -
obs--100 %

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